grit complement
Return intervals NOT covered by the input BED file.
Usage
grit complement [OPTIONS] -i <INPUT> -g <GENOME>
Options
| Option | Description |
|---|---|
-i, --input <FILE> | Input BED file |
-g, --genome <FILE> | Genome file (chromosome sizes) |
--assume-sorted | Assume input is sorted (O(1) memory streaming) |
Examples
Basic complement
# Get regions NOT covered by input
grit complement -i covered.bed -g genome.txt > gaps.bed
# With sorted input (faster, less memory)
grit complement -i sorted.bed -g genome.txt --assume-sorted > gaps.bed
Find intergenic regions
# Get regions between genes
grit complement -i genes.bed -g genome.txt > intergenic.bed
Find uncovered regions
# Find gaps in sequencing coverage
grit complement -i covered_regions.bed -g genome.txt > uncovered.bed
Genome File Format
chr1 248956422
chr2 242193529
chr3 198295559
Output
Input (covered.bed):
chr1 100 200
chr1 300 400
Genome (genome.txt):
chr1 500
Output (gaps):
chr1 0 100
chr1 200 300
chr1 400 500
Visual Example
Chromosome: |----------------------------------------|
0 500
Input: |-----| |-----|
100-200 300-400
Complement: |----| |-----| |-----------------|
0-100 200-300 400-500
Use Cases
Intergenic regions
grit complement -i genes.bed -g genome.txt > intergenic.bed
Coverage gaps
grit complement -i aligned_regions.bed -g genome.txt > gaps.bed
Accessible chromatin (inverse of closed)
grit complement -i closed_chromatin.bed -g genome.txt > open.bed
Performance
# Streaming mode with sorted input
grit complement -i sorted.bed -g genome.txt --assume-sorted